Shimada, T., Ogasawara, H., Kobayashi, I. and Ishihama, A. Genomic SELEX screening of regulatory targets of transcription factors. Methods Mol Biol. 2819, 77-102 (2024)
島田友裕「ゲノム転写制御ネットワーク解析から明らかになる微生物の仕組み」化学と生物 62 (2024)
Saito, S., Kobayashi, I., Hoshiha, M., Uenaka, E., Sakurai, A., Imamura, S. and Shimada, T. Regulatory role of GgaR (YegW) for glycogen accumulation in Escherichia coli K-12. Microorganisms. 12, 115 (2024)
明治大学プレスリリース
「腸内細菌のグリコーゲン蓄積を制御する新規転写因子を同定 ～微生物の炭素源代謝の理解や物質生産への応用に期待～」
Nagao, Y., Koh, S., Taguchi, S. and Shimada, T. Cell-growth phase-dependent promoter replacement approach for improved poly(lactate-co-3-hydroxybutyrate) production in Escherichia coli. Microbial Cell Factories. 22, 10.1186/s12934-023-02143-w (2023)
明治大学プレスリリース
「プロモーター置換法は、 進化型ポリ乳酸の生産性向上に有効であることを実証 ～脱炭素社会に向けて、バイオプラスチック開発技術への貢献に期待～」
Anzai, T., Kijima, K., Fujimori, M., Nakamoro, S., Ishihama, A. and Shimada, T. Expanded roles of lactate-sensing LldR in transcription regulation of the Escherichia coli K-12 genome: lactate utilisation and acid resistance. Microbial Genomics. 9, mgen.0.001015 (2023)
明治大学プレスリリース
「腸内細菌の新規な乳酸応答機構を同定～腸内環境の理解や乳酸菌を含む食品への応用に期待～」
Shimada, T. and Yoshida, H. Overview of the Molecular Mechanism of Bacterial Environmental Adaptation by Comprehensive Analysis. International Journal of Molecular Sciences. 24, 7602 (2023)
Yoshida, H., Shimada, T., Ishihama, A. Metal-responsive transcription factors co-regulate anti-sigma factor (Rsd) and ribosome dimerization factor expression. International Journal of Molecular Sciences. 24, 4717 (2023)
Takada, T., Kijima, K., Ishiguro, A., Ishihama, A. and Shimada, T. Genomic SELEX reveals pervasive role of the flagella master regulator FlhDC in carbon metabolism. International Journal of Molecular Sciences. 24, 3696 (2023)
明治大学プレスリリース
「微生物の運動性とエネルギー生産の協調的制御機構を同定～微生物の病原性の理解や物質生産への応用に期待～」
Kobayashi, I., Mochizuki, K., Teramoto, J., Imamura, S., Takaya, K., Ishihama, A. and Shimada, T. Transcription factor SrsR (YgfI) is a novel regulator for the stress-response genes in stationary phase in Escherichia coli K-12. International Journal of Molecular Sciences. 23, 6055 (2022)
明治大学プレスリリース
「微生物の定常期ストレス応答のための新規転写因子を同定～微生物の自然環境下における生存の理解・応用に期待～」
Shimada, T., Murayama, R., Mashima, T., Kawano, N. and Ishihama, A. Regulatory role of CsuR (YiaU) in determination of cell surface properties of Escherichia coli K-12. Microbiology. 168, doi: 10.1099/mic.0.001166. (2022)
Shimada, T., Furuhata, S. and Ishihama, A. Whole set of constitutive promoters for RpoN sigma factor and the regulatory role of its enhancer protein NtrC in Escherichia coli K-12. Microbial Genomics. 7, mgen000653 (2021)
明治大学プレスリリース
「RNA合成酵素は遺伝子発現に抑制的にも作用することを発見～ゲノム機能を利用した他の分野での応用にも期待～」
Ishihama, A. and Shimada, T. Hierarchy of transcription factor network in Escherichia coli K-12: H-NS mediated genome silencing and anti-silencing by global regulators. FEMS Microbiology Reviews. 45, fuab032 (2021)
Shimada, T., Ogasawara, H., Kobayashi, I., Kobayashi, N. and Ishihama, A. Single-target regulators constitute the minority group of transcription factors in Escherichia coli K-12. Frontiers in Microbiology. 12, 697803 (2021)
Shimada, T., Nakazawa, K., Tachikawa, T., Saito, N., Niwa, T., Taguchi, H. and Tanaka, K. Acetate overflow metabolism regulates a major metabolic shift after glucose depletion in Escherichia coli. FEBS Lett. 595, 2047-2056 (2021)
Sharma, M., Abayakoon, P., Epa, R., Jin, Y., Lingford, JP., Shimada, T., Nakano, M., Mui, JWY., Ishihama, A., Boddard-Borger, ED., Davies GJ. and Williams, SJ. Molecular basis of sulfosugar selectivity in sulfoglycolysis. ACS Cent Sci. 7, 476-487 (2021)
Anzai, T., Imamura, S., Ishihama, A. and Shimada, T. Expanded roles of pyruvate- sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility. Microbial Genomics. 6, mgen000442 (2020)
明治大学 プレスリリース
「～微生物の物質生産能力の向上にも期待～ピルビン酸応答転写因子の微生物における新規な役割を同定」
Ogasawara, H., Ishizuka, T., Hotta, S., Aoki, M., Shimada, T. and Ishihama, A. Novel regulators of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli K-12. Microbiology. 166, 880-890 (2020)
Shimizu, T., Yasuda, R., Mukai, Y., Tanoue, R., Shimada, T., Imamura, S., Tanaka, K., Watanabe, S. and Masuda, T. Proteomic analysis of heme-binding protein from Arabidopsis thaliana and Cyanidioschyzon merolae. Philosophical transactions of the royal society B. 375, 20190488 (2020)
Ogasawara, H., Ishizuka, T., Yamaji, K., Kato, Y., Shimada, T. and Ishihama, A. Regulatory role of pyruvate-sensing BtsSR in biofilm formation by Escherichia coli K-12. FEMS Microbiology letters. 366, pii: fnz251 (2019)
Shimada, T., Yokoyama, Y., Anzai, T., Yamamoto, K. and Ishihama, A. Regulatory role of PlaR (YiaJ) for plant utilization in Escherichia coli K-12. Scientific Reports. 9, 20415 (2019)
https://doi.org/10.1038/s41598-019-56886-x
明治大学 プレスリリース
「植物由来の化合物を効率的に利用し、植物に依存して生存するための微生物のグローバルレギュレーターを発見」
Shimada, T., Yamamoto, K., Nakano, M., Watanabe, H., Schleheck, D. and Ishihama, A. Regulatory role of CsqR (YihW) in transcription of the genes for catabolism of the anionic sugar sulfoquinovose (SQ) in Escherichia coli K-12. Microbiology. 165, 78-89 (2019)
Yoshida, H., Wada, A., Shimada, T., Maki, Y. and Ishihama, A. Coordinated regulation of Rsd and RMF for simultaneous hibernation of transcription apparatus and translation machinery in stationary-phase Escherichia coli. Frontiers in Genetics. 10, 1153 (2019)
Shimizu, T., Kacprzak, S. M., Mochizuki, N., Watanabe, S., Shimada, T., Tanaka, K., Hayashi, Y., Arai, M., Leister, D., Okamoto, H., Terry, M. J. and Masuda, T. The retrograde signaling protein GUN1 regulates tetrapyrrole biosynthesis. Proc Natl Acad Sci USA. 116, 24900-24906 (2019)
Akanuma, G., Tagana, T., Sawada, M., Suzuki, S., Shimada, T., Tanaka, K., Kawamura, F. and Kato-Yamada, Y. C-terminal regulatory domain of the ε subunit of Fo F1 ATP synthase enhances the ATP-dependent H+ pumping that is involved in the maintenance of cellular membrane potential in Bacillus subtilis. Microbyilogyopen. 8, e00815 (2019)
Shimada, T., Ogasawara, H. and Ishihama, A. Genomic SELEX screening of regulatory targets of Escherichia coli transcription factors. Methods Mol Biol. 1837, 49-69 (2018)
Yoshida, H., Shimada, T. and Ishihama, A. Coordinated hibernation of transcriptional and translational apparatus during growth transition of Escherichia coli to stationary phase. mSystems. 3, e00057-18. doi: 10.1128/mSystems.00057-18. (2018)
Shimada, T., Ogasawara, H. and Ishihama, A. Single-target regulators form a minor group of transcription factors in Escherichia coli K-12. Nucleic Acids Res. 46, 3921-3936. https://doi.org/10.1093/nar/gky138 (2018)
明治大学 プレスリリース
「明治大学 農学部 農芸化学科 島田友裕専任講師ら 大腸菌の転写制御ネットワークの全体像を解明」
Yamamoto, K., Yamanaka, Y., Shimada, T., Sarkar, P., Yoshida, M., Bharadwaj, N., Watanabe, H., Taira, Y., Chatterji, D. and Ishihama A. Altered distribution of RNA polymerase lacking the omega subunit within the prophages along the Escherichia coli K-12 genome. mSystems. 3, e00172-17. doi: 10.1128/mSystems.00172-17 (2018)
Shimada, T., Momiyama, E., Yamanaka, Y., Watanabe, H., Yamamoto, K. and Ishihama, A. Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12. FEMS Microbiology Letters. https://doi.org/10.1093/femsle/fnx220 (2017)
Shimada, T., Tanaka, K. and Ishihama, A. The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase. PLoS ONE. 12, e0179181 (2017)
Sugino, H., Usui, T., Shimada, T., Nakano, M., Ogasawara, H., Ishihama, A. and Hirata, A. A structural sketch of RcdA, a transcription factor controlling the master regulator of biofilm formation. FEBS Letters. doi:10.1002/1873-3468.12713 (2017)
Sugimoto, R., Saito, N., Shimada, T. and Tanaka, K. Identification of YbhA as the pyridoxal 5′-phosphate (PLP) phosphatase in Escherichia coli: Importance of PLP homeostasis on the bacterial growth. J. Gen. Appl. Microbiol. https://doi.org/10.2323/jgam.2017.02.008 (2017)
Kobayashi, I., Watanabe, S., Kanesaki, Y., Shimada, T., Yoshikawa, H. and Tanaka, K. Conserved two-component Hik34-Rre1 module directly activates heat-stress inducible transcription of major chaperone and other genes in Synechococcus elongatus PCC 7942. Mol Microbiol.104, 260-277 (2017)
Shimada, T. and Tanaka, K. Use of a bacterial luciferase monitoring system to estimate real-time dynamics of intracellular metabolism in Escherichia coli. Appl Environ Microbiol. 82, 5960-5968 (2016)
Shimada, T., Tanaka, K. and Ishihama, A. Transcription factor DecR (YbaO) controls detoxification of L-cysteine in Escherichia coli. Microbiology. 162, 1698-1707 (2016)
Takada, H., Shimada, T., Dey, D., Quyyum, MZ., Nakano, M., Ishiguro, A., Yoshida, H., Yamamoto, K., Sen, R. and Ishihama A. Differential regulation of rRNA and tRNA transcription from the rRNA-tRNA composite operon in Escherichia coli. PLoS ONE. 11, e0163057 (2016)
Ishihama, A., Shimada, T. and Yamazaki, Y. Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. Nucleic Acids Res. 44, 2058-2074 (2016)
Sharma, R., Shimada, T., Mishra, VK., Upreti, S. and Sardesai, AA. Growth inhibition by external potassium of Escherichia coli lacking PtsN (EIIANtr) is caused by potassium limitation mediated by YcgO. J Bacteriol. 198, 1868-1882 (2016)
Yamanaka, Y., Shimada, T., Yamamoto, K. and Ishihama, A. Transcription factor CecR (YbiH) regulates a set of genes affecting the sensitivity of Escherichia coli against cefoperazone and chloramphenicol. Microbiology. 162, 1253-1264 (2016)
Shimada, T., Takada, H., Yamamoto, K. and Ishihama, A. Expanded roles of two-component response regulator OmpR in Escherichia coli: Genomic SELEX search for novel regulation targets. Genes Cells. 20, 915-931 (2015)
Shimada, T., Saito, N., Maeda, M., Tanaka, K. and Ishihama, A. Expanded roles of leucine-responsive regulatory protein in transcription regulation of the Escherichia coli genome: Genomic SELEX screening of the regulation targets. Microbial Genomics. 1, 1-19. (2015)
Maeda, M., Shimada, T. and Ishihama, A. Strength and regulation of seven rRNA promoters in Escherichia coli. PLoS ONE.10, e0144697. (2015)
Shimada, T., Yamazaki, Y., Tanaka, K. and Ishihama, A. The Whole Set of Constitutive Promoters Recognized by RNA polymerase RpoD Holoenzyme of Escherichia coli. PLoS ONE. 9, e90447. (2014)
Shimada, T., Shimada, K., Matsui, M., Kitai, Y., Igarashi, J., Suga, H. and Ishihama, A. Roles of Cell Division Control Factor SdiA: Recognition of Quorum Sensing Signals and Modulation of Transcription Regulation Targets. Genes Cells. 19, 405-18. (2014)
Conway, T., Creecy, J. P., Maddox, S. M., Grissom, J. E., Conkle, T. L., Shadid, T. M., Teramoto, J., San, Miguel, P., Shimada, T., Ishihama, A., Mori, H. and Wanner B. L. Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing. MBio. 5, e01442-14. (2014)
Ishihama, A., Kori, A., Koshio, E., Yamada, K., Maeda, H., Shimada, T., Makinoshima, H., Iwata, A. and Fujita, N. Intracellular Concentrations of Transcription Factors in Escherichia coli: 65 species with known regulatory functions. Journal of Bacteriology. 196, 2718-27. (2014)
Nakano, M., Ogasawara, H., Shimada, T., Yamamoto, K. and Ishihama, A. Involvement of cAMP-CRP in transcription activation and repression of the pck gene encoding PEP carboxykinase, the key enzyme of gluconeogenesis. FEMS Microbiology Letters. 355, 93-9. (2014)
Shimada, T., Kori, A. and Ishihama, A. Involvement of the Ribose operon Repressor RbsR in Regulation of Purine Nucleotide Synthesis in Escherichia coli. FEMS Microbiology Letters. 344, 159-65. (2013)
Shimada, T., Yoshida, H. and Ishihama, A. Involvement of Cyclic AMP Receptor Protein in Regulation of the rmf Gene Encoding the Ribosome Modulation Factor in Escherichia coli. Journal of Bacteriology. 195, 2212-2219. (2013)
Shimada, T., Yamazaki, K. and Ishihama, A. A novel regulator PgrR for switch control of peptideglycan recycling in Escherichia coli. Genes Cells. 18, 123-134. (2013)
Shimada K, Ogasawara H, Yamada K, Shimura M, Kori A, Shimada T, Yamanaka Y, Yamamoto K, Ishihama A. Screening of Promoter-Specific Transcription Factors: Multiple Regulators for the sdiA Gene Involved in Cell Division Control and Quorum Sensing. Microbiology.159, 2501-2512. (2013)
Shimada, T., Katayama, Y., Kawakita, S., Ogasawara, H., Nakano, M., Yamamoto, K. and Ishihama, A. A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli. MicrobiologyOpen. 1, 381-394. (2012)
Shimada, T., Bridier, A., Briandet, R. and Ishihama, A.: Novel roles of LeuO in transcription regulation of E.coli genome: antagonistic interplay with the universal silencer H-NS. Mol Microbiol. 82, 378-97. (2011)
Shimada, T., Yamamoto, K., Fujita, N. and Ishihama, A.: Novel Members of the cAMP Receptor Protein (CRP) Regulon for Transport and Metabolism of Carbon Sources. PLoS ONE. 6, e20081. (2011).
Shimada, T., Yamamoto, K. and Ishihama, A.: Novel Members of the Cra Regulon Involved in Carbon Metabolism in Escherichia coli. Journal of Bacteriology. 193, 649-659 (2011).
Shimada, T., Yamamoto, K. and Ishihama, A.: Involvement of the leucine response transcription factor LeuO in regulation of the genes for sulfa drug efflux. Journal of Bacteriology. 191, 4562-4571 (2009)
Shimada, T., Fujita, N., Yamamoto, K. and Ishihama, A.: Genomic SELEX for the genome-wide search of regulation targets by transcription factors: SELEX-clos and SELEX-chip procedures. Micro- and Nano-Mechatronics and Human Science, 2009 IEEE International Symposium on Nov. (Fukuda, T. et al., eds), IEEE Robotics and Automation Society, USA. 259-261 (2009)
Teramoto, J., Yamanishi, Y., Magdy, E-S.H., Hasegawa, A., Nakajima, M., Shimada, T., Arai, F., Fukuda, T. and Ishihama, A.: Single live-bacterial cell assay of promoter activity and regulation: Escherichia coli gcl promoter. . In: Proc. 2009 Internatl. Symp. Micro-Nano Mechatronics Human Sci. (Fukuda, T. et al., eds), 175-178 (2009)
Shimada T, Ishihama A, Busby SJ, Grainger DC.: The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acid Research. 36, 3950-5 (2008)
Umezawa Y, Shimada T, Kori A, Yamada K, Ishihama A.: The uncharacterized transcription factor YdhM is the regulator of the nemA gene, encoding N-ethylmaleimide reductase. Journal of Bacteriology. 190, 5890-7 (2008)
Yamamoto, K., Shimada, T. and Ishihama, A.: Comprehensive analysis for the recognition sequences of DNA-binding transcription factors within the E. coli genome using the newly developed ‘Promoter Chip’. Micro- and Nano-Mechatronics and Human Science, 2008 IEEE International Symposium on Nov. IEEE Robotics and Automation Society, USA. 307-310 (2008)
Shimada T, Hirao K, Kori A, Yamamoto K, Ishihama A.: RutR is the uracil/thymine -sensing master regulator of a set of genes for synthesis and degradation of pyrimidines. Molecular Microbiology. 66, 744-57 (2007)
Yang J, Ogawa Y, Camakaris H, Shimada T, Ishihama A, Pittard AJ.: folA, a new member of the TyrR regulon in Escherichia coli K-12. Journal of Bacteriology. 189, 6080-4 (2007)
Chatterji D, Ogawa Y, Shimada T, Ishihama A.: The role of the omega subunit of RNA polymerase in expression of the relA gene in Escherichia coli. FEMS Microbiology Letters. 267, 51-5 (2007)
Ishihama, A., Ogasawara, H., Shimada, T., Teramoto, J., Hasegawa, Y., Umezawa, K., Yabuki, Y., ishida, T., Inaba, M., Kori, K., Yamada, K., Kitai, Y., Kobayashi, N., Kato, D., and Yamamoto, K.: Multi-scale genetics of transcription network: understanding the regulatory roles of all 300 transcription factors from a single organism Escherichia coli. Micro- and Nano-Mechatronics and Human Science, 2007 IEEE International Symposium on Nov. IEEE Robotics and Automation Society, USA. 21-27 (2007)
Shimada T, Fujita N, Maeda M, Ishihama A.: Systematic search for the Cra-binding promoters using genomic SELEX system. Genes to Cells. 10, 907-18 (2005)
Shimada T, Makinoshima H, Ogawa Y, Miki T, Maeda M, and Ishihama A.: Classification and strength measurement of stationary phase promoters by use of a newly developed promoter cloning vector. Journal of Bacteriology. 186, 7112-22 (2004)